Recommendations for the use of next-generation sequencing (NGS) for patients with metastatic cancers: a report from the ESMO Precision Medicine Working Group

Next-generation sequencing (NGS) allows sequencing of a high number of nucleotides in a short time frame at an affordable cost. While this technology has been widely implemented, there are no recommendations from scientific societies about its use in oncology practice. The European Society for Medical Oncology (ESMO) is proposing three levels of recommendations for the use of NGS. Based on the current evidence, ESMO recommends routine use of NGS on tumour samples in advanced non-squamous non-small-cell lung cancer (NSCLC), prostate cancers, ovarian cancers and cholangiocarcinoma. In these tumours, large multigene panels could be used if they add acceptable extra cost compared with small panels. In colon cancers, NGS could be an alternative to PCR. In addition, based on the KN158 trial and considering that patients with endometrial and small-cell lung cancers should have broad access to anti-programmed cell death 1 (anti-PD1) antibodies, it is recommended to test tumour mutational burden (TMB) in cervical cancers, well- and moderately-differentiated neuroendocrine tumours, salivary cancers, thyroid cancers and vulvar cancers, as TMB-high predicted response to pembrolizumab in these cancers. Outside the indications of multigene panels, and considering that the use of large panels of genes could lead to few clinically meaningful responders, ESMO acknowledges that a patient and a doctor could decide together to order a large panel of genes, pending no extra cost for the public health care system and if the patient is informed about the low likelihood of benefit. ESMO recommends that the use of off-label drugs matched to genomics is done only if an access programme and a procedure of decision has been developed at the national or regional level. Finally, ESMO recommends that clinical research centres develop multigene sequencing as a tool to screen patients eligible for clinical trials and to accelerate drug development, and prospectively capture the data that could further inform how to optimise the use of this technology

NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics

Xenarthrans – anteaters, sloths, and armadillos – have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with 24 domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, ten anteaters, and six sloths. Our dataset includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data-paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the south of the USA, Mexico, and Caribbean countries at the northern portion of the Neotropics, to its austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n=5,941), and Cyclopes sp. has the fewest (n=240). The armadillo species with the most data is Dasypus novemcinctus (n=11,588), and the least recorded for Calyptophractus retusus (n=33). With regards to sloth species, Bradypus variegatus has the most records (n=962), and Bradypus pygmaeus has the fewest (n=12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other datasets of Neotropical Series which will become available very soon (i.e. Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans dataset

Population and fertility by age and sex for 195 countries and territories, 1950–2017: a systematic analysis for the Global Burden of Disease Study 2017

Background: Population estimates underpin demographic and epidemiological research and are used to track progress on numerous international indicators of health and development. To date, internationally available estimates of population and fertility, although useful, have not been produced with transparent and replicable methods and do not use standardised estimates of mortality. We present single-calendar year and single-year of age estimates of fertility and population by sex with standardised and replicable methods. Methods: We estimated population in 195 locations by single year of age and single calendar year from 1950 to 2017 with standardised and replicable methods. We based the estimates on the demographic balancing equation, with inputs of fertility, mortality, population, and migration data. Fertility data came from 7817 location-years of vital registration data, 429 surveys reporting complete birth histories, and 977 surveys and censuses reporting summary birth histories. We estimated age-specific fertility rates (ASFRs; the annual number of livebirths to women of a specified age group per 1000 women in that age group) by use of spatiotemporal Gaussian process regression and used the ASFRs to estimate total fertility rates (TFRs; the average number of children a woman would bear if she survived through the end of the reproductive age span [age 10–54 years] and experienced at each age a particular set of ASFRs observed in the year of interest). Because of sparse data, fertility at ages 10–14 years and 50–54 years was estimated from data on fertility in women aged 15–19 years and 45–49 years, through use of linear regression. Age-specific mortality data came from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 estimates. Data on population came from 1257 censuses and 761 population registry location-years and were adjusted for underenumeration and age misreporting with standard demographic methods. Migration was estimated with the GBD Bayesian demographic balancing model, after incorporating information about refugee migration into the model prior. Final population estimates used the cohort-component method of population projection, with inputs of fertility, mortality, and migration data. Population uncertainty was estimated by use of out-of-sample predictive validity testing. With these data, we estimated the trends in population by age and sex and in fertility by age between 1950 and 2017 in 195 countries and territories. Findings: From 1950 to 2017, TFRs decreased by 49\ub74% (95% uncertainty interval [UI] 46\ub74–52\ub70). The TFR decreased from 4\ub77 livebirths (4\ub75–4\ub79) to 2\ub74 livebirths (2\ub72–2\ub75), and the ASFR of mothers aged 10–19 years decreased from 37 livebirths (34–40) to 22 livebirths (19–24) per 1000 women. Despite reductions in the TFR, the global population has been increasing by an average of 83\ub78 million people per year since 1985. The global population increased by 197\ub72% (193\ub73–200\ub78) since 1950, from 2\ub76 billion (2\ub75–2\ub76) to 7\ub76 billion (7\ub74–7\ub79) people in 2017; much of this increase was in the proportion of the global population in south Asia and sub-Saharan Africa. The global annual rate of population growth increased between 1950 and 1964, when it peaked at 2\ub70%; this rate then remained nearly constant until 1970 and then decreased to 1\ub71% in 2017. Population growth rates in the southeast Asia, east Asia, and Oceania GBD super-region decreased from 2\ub75% in 1963 to 0\ub77% in 2017, whereas in sub-Saharan Africa, population growth rates were almost at the highest reported levels ever in 2017, when they were at 2\ub77%. The global average age increased from 26\ub76 years in 1950 to 32\ub71 years in 2017, and the proportion of the population that is of working age (age 15–64 years) increased from 59\ub79% to 65\ub73%. At the national level, the TFR decreased in all countries and territories between 1950 and 2017; in 2017, TFRs ranged from a low of 1\ub70 livebirths (95% UI 0\ub79–1\ub72) in Cyprus to a high of 7\ub71 livebirths (6\ub78–7\ub74) in Niger. The TFR under age 25 years (TFU25; number of livebirths expected by age 25 years for a hypothetical woman who survived the age group and was exposed to current ASFRs) in 2017 ranged from 0\ub708 livebirths (0\ub707–0\ub709) in South Korea to 2\ub74 livebirths (2\ub72–2\ub76) in Niger, and the TFR over age 30 years (TFO30; number of livebirths expected for a hypothetical woman ageing from 30 to 54 years who survived the age group and was exposed to current ASFRs) ranged from a low of 0\ub73 livebirths (0\ub73–0\ub74) in Puerto Rico to a high of 3\ub71 livebirths (3\ub70–3\ub72) in Niger. TFO30 was higher than TFU25 in 145 countries and territories in 2017. 33 countries had a negative population growth rate from 2010 to 2017, most of which were located in central, eastern, and western Europe, whereas population growth rates of more than 2\ub70% were seen in 33 of 46 countries in sub-Saharan Africa. In 2017, less than 65% of the national population was of working age in 12 of 34 high-income countries, and less than 50% of the national population was of working age in Mali, Chad, and Niger. Interpretation: Population trends create demographic dividends and headwinds (ie, economic benefits and detriments) that affect national economies and determine national planning needs. Although TFRs are decreasing, the global population continues to grow as mortality declines, with diverse patterns at the national level and across age groups. To our knowledge, this is the first study to provide transparent and replicable estimates of population and fertility, which can be used to inform decision making and to monitor progress. Funding: Bill & Melinda Gates Foundation

Brazilian Flora 2020: Leveraging the power of a collaborative scientific network

International audienceThe shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiversity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxonomic impediment to biodiversity research and conservation planning. The taxonomic impediment and the biodiversity crisis are widely recognized, highlighting the urgent need for reliable taxonomic data. Over the past decade, numerous countries worldwide have devoted considerable effort to Target 1 of the Global Strategy for Plant Conservation (GSPC), which called for the preparation of a working list of all known plant species by 2010 and an online world Flora by 2020. Brazil is a megadiverse country, home to more of the world's known plant species than any other country. Despite that, Flora Brasiliensis, concluded in 1906, was the last comprehensive treatment of the Brazilian flora. The lack of accurate estimates of the number of species of algae, fungi, and plants occurring in Brazil contributes to the prevailing taxonomic impediment and delays progress towards the GSPC targets. Over the past 12 years, a legion of taxonomists motivated to meet Target 1 of the GSPC, worked together to gather and integrate knowledge on the algal, plant, and fungal diversity of Brazil. Overall, a team of about 980 taxonomists joined efforts in a highly collaborative project that used cybertaxonomy to prepare an updated Flora of Brazil, showing the power of scientific collaboration to reach ambitious goals. This paper presents an overview of the Brazilian Flora 2020 and provides taxonomic and spatial updates on the algae, fungi, and plants found in one of the world's most biodiverse countries. We further identify collection gaps and summarize future goals that extend beyond 2020. Our results show that Brazil is home to 46,975 native species of algae, fungi, and plants, of which 19,669 are endemic to the country. The data compiled to date suggests that the Atlantic Rainforest might be the most diverse Brazilian domain for all plant groups except gymnosperms, which are most diverse in the Amazon. However, scientific knowledge of Brazilian diversity is still unequally distributed, with the Atlantic Rainforest and the Cerrado being the most intensively sampled and studied biomes in the country. In times of “scientific reductionism”, with botanical and mycological sciences suffering pervasive depreciation in recent decades, the first online Flora of Brazil 2020 significantly enhanced the quality and quantity of taxonomic data available for algae, fungi, and plants from Brazil. This project also made all the information freely available online, providing a firm foundation for future research and for the management, conservation, and sustainable use of the Brazilian funga and flora

Growing knowledge: an overview of Seed Plant diversity in Brazil

Abstract An updated inventory of Brazilian seed plants is presented and offers important insights into the country's biodiversity. This work started in 2010, with the publication of the Plants and Fungi Catalogue, and has been updated since by more than 430 specialists working online. Brazil is home to 32,086 native Angiosperms and 23 native Gymnosperms, showing an increase of 3% in its species richness in relation to 2010. The Amazon Rainforest is the richest Brazilian biome for Gymnosperms, while the Atlantic Rainforest is the richest one for Angiosperms. There was a considerable increment in the number of species and endemism rates for biomes, except for the Amazon that showed a decrease of 2.5% of recorded endemics. However, well over half of Brazillian seed plant species (57.4%) is endemic to this territory. The proportion of life-forms varies among different biomes: trees are more expressive in the Amazon and Atlantic Rainforest biomes while herbs predominate in the Pampa, and lianas are more expressive in the Amazon, Atlantic Rainforest, and Pantanal. This compilation serves not only to quantify Brazilian biodiversity, but also to highlight areas where there information is lacking and to provide a framework for the challenge faced in conserving Brazil's unique and diverse flora

Measurement of the Higgs boson inclusive and differential fiducial production cross sections in the diphoton decay channel with pp collisions at s \sqrt{s} = 13 TeV

International audienceThe measurements of the inclusive and differential fiducial cross sections of the Higgs boson decaying to a pair of photons are presented. The analysis is performed using proton-proton collisions data recorded with the CMS detector at the LHC at a centre-of-mass energy of 13 TeV and corresponding to an integrated luminosity of 137 fb$^{−1}$. The inclusive fiducial cross section is measured to be ${\sigma}_{\textrm{fid}}={73.4}_{-5.3}^{+5.4}{\left(\textrm{stat}\right)}_{-2.2}^{+2.4}\left(\textrm{syst}\right)$ fb, in agreement with the standard model expectation of 75.4 ± 4.1 fb. The measurements are also performed in fiducial regions targeting different production modes and as function of several observables describing the diphoton system, the number of additional jets present in the event, and other kinematic observables. Two double differential measurements are performed. No significant deviations from the standard model expectations are observed.[graphic not available: see fulltext

Search for Higgs boson decays to a Z boson and a photon in proton-proton collisions at s \sqrt{s} = 13 TeV

International audienceResults are presented from a search for the Higgs boson decay H → Zγ, where Z → ℓ$^{+}$ℓ$^{−}$ with ℓ = e or μ. The search is performed using a sample of proton-proton (pp) collision data at a center-of-mass energy of 13 TeV, recorded by the CMS experiment at the LHC, corresponding to an integrated luminosity of 138 fb$^{−1}$. Events are assigned to mutually exclusive categories, which exploit differences in both event topology and kinematics of distinct Higgs production mechanisms to enhance signal sensitivity. The signal strength μ, defined as the product of the cross section and the branching fraction \left[\sigma \left(\textrm{pp}\to \textrm{H}\right)\mathcal{B}\left(\textrm{H}\to \textrm{Z}\upgamma \right)\right] relative to the standard model prediction, is extracted from a simultaneous fit to the ℓ$^{+}$ℓ$^{−}$γ invariant mass distributions in all categories and is measured to be μ = 2.4 ± 0.9 for a Higgs boson mass of 125.38 GeV. The statistical significance of the observed excess of events is 2.7 standard deviations. This measurement corresponds to \left[\sigma \left(\textrm{pp}\to \textrm{H}\right)\mathcal{B}\left(\textrm{H}\to \textrm{Z}\upgamma \right)\right]=0.21\pm 0.08 pb. The observed (expected) upper limit at 95% confidence level on μ is 4.1 (1.8), where the expected limit is calculated under the background-only hypothesis. The ratio of branching fractions \mathcal{B}\left(\textrm{H}\to \textrm{Z}\upgamma \right)/\mathcal{B}\left(\textrm{H}\to \upgamma \upgamma \right) is measured to be ${1.5}_{-0.6}^{+0.7}$, which agrees with the standard model prediction of 0.69 ± 0.04 at the 1.5 standard deviation level.[graphic not available: see fulltext

Search for heavy resonances and quantum black holes in eμ\mu, eτ\tau, and μτ\mu\tau final states in proton-proton collisions at s\sqrt{s} = 13 TeV

A search is reported for heavy resonances and quantum black holes decaying into e$\mu$, e$\tau$, and $\mu\tau$ final states in proton-proton collision data recorded by the CMS experiment at the CERN LHC during 2016-2018 at $\sqrt{s} =$ 13 TeV, corresponding to an integrated luminosity of 138 fb$^{-1}$. The e$\mu$, e$\tau$, and $\mu\tau$ invariant mass spectra are reconstructed, and no evidence is found for physics beyond the standard model. Upper limits are set at 95% confidence level on the product of the cross section and branching fraction for lepton flavor violating signals. Three benchmark signals are studied: resonant $\tau$ sneutrino production in $R$ parity violating supersymmetric models, heavy Z' gauge bosons with lepton flavor violating decays, and nonresonant quantum black hole production in models with extra spatial dimensions. Resonant $\tau$ sneutrinos are excluded for masses up to 4.2 TeV in the e$\mu$ channel, 3.7 TeV in the e$\tau$ channel, and 3.6 TeV in the $\mu\tau$ channel. A Z' boson with lepton flavor violating couplings is excluded up to a mass of 5.0 TeV in the e$\mu$ channel, up to 4.3 TeV in the e$\tau$ channel, and up to 4.1 TeV in the $\mu\tau$ channel. Quantum black holes in the benchmark model are excluded up to the threshold mass of 5.6 TeV in the e$\mu$ channel, 5.2 TeV in the e$\tau$ channel, and 5.0 TeV in the $\mu\tau$ channel. In addition, model-independent limits are extracted to allow comparisons with other models for the same final states and similar event selection requirements. The results of these searches provide the most stringent limits available from collider experiments for heavy particles that undergo lepton flavor violating decays.A search is reported for heavy resonances and quantum black holes decaying into eμ, eτ, and μτ final states in proton-proton collision data recorded by the CMS experiment at the CERN LHC during 2016–2018 at $\sqrt{s}$ = 13 TeV, corresponding to an integrated luminosity of 138 fb$^{−1}$. The eμ, eτ, and μτ invariant mass spectra are reconstructed, and no evidence is found for physics beyond the standard model. Upper limits are set at 95% confidence level on the product of the cross section and branching fraction for lepton flavor violating signals. Three benchmark signals are studied: resonant τ sneutrino production in R parity violating supersymmetric models, heavy Z′ gauge bosons with lepton flavor violating decays, and nonresonant quantum black hole production in models with extra spatial dimensions. Resonant τ sneutrinos are excluded for masses up to 4.2TeV in the eμ channel, 3.7TeV in the eτ channel, and 3.6TeV in the μτ channel. A Z′ boson with lepton flavor violating couplings is excluded up to a mass of 5.0TeV in the eμ channel, up to 4.3Te V in the eτ channel, and up to 4.1TeV in the μτ channel. Quantum black holes in the benchmark model are excluded up to the threshold mass of 5.6TeV in the eμ channel, 5.2TeV in the eτ channel, and 5.0TeV in the μτ channel. In addition, model-independent limits are extracted to allow comparisons with other models for the same final states and similar event selection requirements. The results of these searches provide the most stringent limits available from collider experiments for heavy particles that undergo lepton flavor violating decays.[graphic not available: see fulltext]A search is reported for heavy resonances and quantum black holes decaying into e$\mu$, e$\tau$, and $\mu\tau$ final states in proton-proton collision data recorded by the CMS experiment at the CERN LHC during 2016-2018 at $\sqrt{s}$ = 13 TeV, corresponding to an integrated luminosity of 138 fb$^{-1}$. The e$\mu$, e$\tau$, and $\mu\tau$ invariant mass spectra are reconstructed, and no evidence is found for physics beyond the standard model. Upper limits are set at 95% confidence level on the product of the cross section and branching fraction for lepton flavor violating signals. Three benchmark signals are studied: resonant $\tau$ sneutrino production in $R$ parity violating supersymmetric models, heavy Z' gauge bosons with lepton flavor violating decays, and nonresonant quantum black hole production in models with extra spatial dimensions. Resonant $\tau$ sneutrinos are excluded for masses up to 4.2 TeV in the e$\mu$ channel, 3.7 TeV in the e$\tau$ channel, and 3.6 TeV in the $\mu\tau$ channel. A Z' boson with lepton flavor violating couplings is excluded up to a mass of 5.0 TeV in the e$\mu$ channel, up to 4.3 TeV in the e$\tau$ channel, and up to 4.1 TeV in the $\mu\tau$ channel. Quantum black holes in the benchmark model are excluded up to the threshold mass of 5.6 TeV in the e$\mu$ channel, 5.2 TeV in the e$\tau$ channel, and 5.0 TeV in the $\mu\tau$ channel. In addition, model-independent limits are extracted to allow comparisons with other models for the same final states and similar event selection requirements. The results of these searches provide the most stringent limits available from collider experiments for heavy particles that undergo lepton flavor violating decays